Computational protocol: Restricted Gene Flow for Gadus macrocephalus from Yellow Sea Based on Microsatellite Markers: Geographic Block of Tsushima Current

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Protocol publication

[…] Deviations from the Hardy-Weinberg equilibrium (HWE) and linkage disequilibrium of each locus within each site were checked by GENEPOP 3.4 []. The number of alleles (A), observed heterozygosity (Ho), expected heterozygosity (He) and Polymorphism Information Content (PIC) were obtained by Microsoft Excel tools []. The null alleles in each population were checked by Micro-Checker 2.2.3 []. The values of pairwise Fst were calculated by FSTAT 2.9.3 []. Bottleneck 1.2.02 program [] was used to detect the evidence of recent bottleneck events under three different mutation models: the infinite allele model (IAM), stepwise mutation model (SMM) and two-phase mutation model (TPM), where 95% single-step mutations and 5% multiple steps mutations with 1000 simulation iterations were set as recommended []. We also proposed a graphical descriptor of the shape of the allele frequency distribution (mode shift indicator) which could differentiate between bottlenecked and stable populations []. ARLEQUIN 3.1 was employed to assess the population structure by the analysis of molecular variance (AMOVA) [], and AMOVA was carried out with different gene pools. In order to detect the suitable groups for AMOVA, Fst measures were subjected to multidimensional scaling (MDS) and plotted in two dimensions (applied using SPSS 11.0 (SPSS Inc., Chicago, IL, USA), data not shown). The relationship between genetic distances and geographic distances was assessed using Reduced Major Axis (RMA) regression and Mantel tests using IBDWS [,]. We calculated the (δμ)2 genetic distance by POPULATION 1.2 [] and constructed the UPGMA tree based on the (δμ)2 genetic distance by MEGA 5 []. Three-dimensional factorial correspondence analysis (3D-FCA) was performed in GENETIX 4.05 to explore population divisions and relationships of Pacific cod, independent from prior knowledge of their relationships []. The possibility of cryptic population structure of Pacific cod was detected by STRUCTURE 2.2 []. Markov chain Monte Carlo (MCMC) consisted of 100,000 burn-in iterations followed by 1,000,000 iterations. The simulated K values ranged from 1 to 10 (total sites). Ten independent runs were implemented for each specific K-value in order to verify the consistency of the results. The ad hoc estimated likelihood of K (ΔK) was used to determine the most likely number of populations (K) based on the rate of change in the log probability of the data (Ln P(D)) []. […]

Pipeline specifications

Software tools Genepop, Arlequin, IBDWS, MEGA
Application Population genetic analysis